Oldest most complete, genetically intact human skeleton in New World

In a paper released today in the journal Science, an international team of researchers and cave divers present the results of an expedition that discovered a near-complete early American human skeleton with an intact cranium and preserved DNA. The remains were found surrounded by a variety of extinct animals more than 40 meters (130 feet) below sea level in Hoyo Negro, a deep pit within the Sac Actun cave system on Mexico’s Yucatán Peninsula.

Photo by Paul Nicklen/National Geographic Divers Alberto Nava and Susan Bird transport the Hoyo Negro skull to an underwater turntable so that it can be photographed in order to create a 3-D model.

The skeletal remains of a teenage female from the late Pleistocene or last ice age found in an underwater cave in Mexico have major implications for our understanding of the origins of the Western Hemisphere’s first people and their relationship to contemporary Native Americans.

In a paper released today in the journal Science, an international team of researchers and cave divers present the results of an expedition that discovered a near-complete early American human skeleton with an intact cranium and preserved DNA. The remains were found surrounded by a variety of extinct animals more than 40 meters (130 feet) below sea level in Hoyo Negro, a deep pit within the Sac Actun cave system on Mexico’s Yucatán Peninsula. The Hoyo Negro project was led by the Mexican government’s National Institute of Anthropology and History (INAH) and supported by the National Geographic Society.

“These discoveries are extremely significant,” said Pilar Luna, INAH’s director of underwater archaeology. “Not only do they shed light on the origins of modern Americans, they clearly demonstrate the paleontological potential of the Yucatán Peninsula and the importance of conserving Mexico’s unique heritage.”

The findings detailed in Science are noteworthy on numerous levels:

This is the first time researchers have been able to match a skeleton with an early American (or Paleoamerican) skull and facial characteristics with DNA linked to the hunter-gatherers who moved onto the Bering Land Bridge from northeast Asia (Beringia) between 26,000 and 18,000 years ago, spreading southward into North America sometime after 17,000 years ago.

Based on a combination of direct radiocarbon dating and indirect dating by the uranium-thorium method, it is one of the oldest skeletons discovered in the New World.

It is clearly the most complete skeleton older than 12,000 years as it includes all of the major bones of the body and an intact cranium and set of teeth.

According to the paper’s lead author, James Chatters of Applied Paleoscience, “This expedition produced some of the most compelling evidence to date of a link between Paleoamericans, the first people to inhabit the Americas after the most recent ice age, and modern Native Americans. What this suggests is that the differences between the two are the result of in situ evolution rather than separate migrations from distinct Old World homelands.”

The field research team endured extremely challenging conditions to access the skeleton’s remote underwater location at the bottom of Hoyo Negro, deep beneath the jungles of the eastern Yucatán Peninsula. The multidisciplinary team, composed of professional divers, archaeologists and paleontologists, extensively documented the bones in situ.

Alberto Nava with Bay Area Underwater Explorers was part of the team that first discovered Hoyo Negro in 2007. “We had no idea what we might find when we initially entered the cave, which is the allure of cave diving,” said Nava. “Needless to say, I am incredibly proud to be part of the efforts to share Hoyo Negro’s story with the world.”

Assessing the skeleton’s age required a novel approach given the challenging environmental conditions. The research team analyzed tooth enamel and bat-dropped seeds using radiocarbon dating and calcite deposits found on the bones using the uranium-thorium method, establishing an age of between 12,000 and 13,000 years. They used similar methodology to date the remains of a variety of gomphothere (an extinct relative of the mastodon) found near the skeleton to around 40,000 years ago. The more than 26 large mammals found at the site included saber-toothed cats and giant ground sloths, which were largely extinct in North America 13,000 years ago. The skeleton’s age was further supported by evidence of rising sea levels, which were as much as 360 feet (120 meters) lower during the last ice age than they are today.

The extremely small skeleton is of a very delicately built woman measuring only 4’10” tall. Named “Naia” by the dive team, she is estimated to have been between 15 and 16 years old at the time of her death, based on the development of her skeleton and teeth.

Analyses of DNA extracted from the skeleton’s wisdom tooth found it belonged to an Asian-derived lineage that occurs only in America (haplogroup D, subhaplogroup D1). Finding a skeleton with DNA from one of America’s founding lineages in Central America greatly expands the geographic distribution of confirmed Beringians among the earliest Americans.

Additional funding for the project was provided by the Archaeological Institute of America, the Waitt Institute, The University of New Mexico, The Pennsylvania State University, The University of Texas at Austin, University of Illinois at Urbana-Champaign and DirectAMS. Researchers from McMaster University, Northwestern University and Washington State University also participated.

The Hoyo Negro expedition will be featured in National Geographic magazine and on a National Geographic Television program airing on the PBS series “NOVA” in 2015.